8OFJ | pdb_00008ofj

Mycoplasma pneumoniae CdaM

X-RAY DIFFRACTION

---

Crystallization

Crystalization Experiments
ID	Method	pH	Temperature	Details
1	VAPOR DIFFUSION, SITTING DROP	7.5	293	25% (v/v) PEG MME 2000 0.1M Na-HEPES pH 7.5

Crystal Properties
Matthews coefficient	Solvent content
1.88	34.7

Crystal Data

Unit Cell
Length ( Å )	Angle ( ˚ )
a = 38.84	α = 90
b = 80.42	β = 93.13
c = 44.444	γ = 90

Symmetry
Space Group	P 1 21 1

Diffraction

Diffraction Experiment
ID #	Crystal ID	Scattering Type	Data Collection Temperature	Detector	Detector Type	Details	Collection Date	Monochromator	Protocol
1	1	x-ray	100	PIXEL	DECTRIS EIGER X 16M		2022-12-14	M	SINGLE WAVELENGTH

Radiation Source
ID #	Source	Type	Wavelength List	Synchrotron Site	Beamline
1	SYNCHROTRON	PETRA III, EMBL c/o DESY BEAMLINE P13 (MX1)	0.97626	PETRA III, EMBL c/o DESY	P13 (MX1)

Data Collection

Overall
ID #	Resolution (High)	Resolution (Low)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Net I Over Average Sigma (I)	Redundancy	Number Reflections (All)	Number Reflections (Observed)	Observed Criterion Sigma (F)	Observed Criterion Sigma (I)	B (Isotropic) From Wilson Plot
1	2.25	50	99.3	0.122	0.132	0.998	11.68	6.9		12934

Highest Resolution Shell
ID #	Resolution (High)	Resolution (Low)	Percent Possible (All)	Percent Possible (Observed)	R Merge I (Observed)	Rrim I (All)	CC (Half)	Mean I Over Sigma (Observed)	Redundancy	Number Unique Reflections (All)
1	2.25	2.31			1.308	1.412	0.639

Refinement

Statistics
Diffraction ID	Structure Solution Method	Cross Validation method	Resolution (High)	Resolution (Low)	Number Reflections (Observed)	Number Reflections (R-Free)	Percent Reflections (Observed)	R-Factor (All)	R-Work (Depositor)	R-Work (DCC)	R-Free (Depositor)	R-Free (DCC)	Mean Isotropic B
X-RAY DIFFRACTION	MOLECULAR REPLACEMENT	FREE R-VALUE	2.25	38.854	12917	669	99.247	0.201	0.1978	0.2	0.2494	0.25	51.813

Temperature Factor Modeling
Anisotropic B[1][1]	Anisotropic B[1][2]	Anisotropic B[1][3]	Anisotropic B[2][2]	Anisotropic B[2][3]	Anisotropic B[3][3]
-0.028		-0.017	0.04		-0.01

RMS Deviations
Key	Refinement Restraint Deviation
r_dihedral_angle_3_deg	17.262
r_dihedral_angle_6_deg	15.718
r_lrange_other	9.826
r_lrange_it	9.821
r_scangle_it	7.68
r_scangle_other	7.678
r_dihedral_angle_1_deg	5.557
r_mcangle_it	5.48
r_mcangle_other	5.478
r_scbond_it	4.965
r_scbond_other	4.964
r_dihedral_angle_2_deg	4.26
r_mcbond_other	3.706
r_mcbond_it	3.705
r_angle_refined_deg	1.085
r_angle_other_deg	0.377
r_symmetry_nbd_other	0.211
r_nbd_refined	0.197
r_nbd_other	0.192
r_symmetry_nbd_refined	0.18
r_nbtor_refined	0.178
r_xyhbond_nbd_refined	0.155
r_symmetry_xyhbond_nbd_refined	0.111
r_symmetry_nbtor_other	0.077
r_chiral_restr	0.051
r_bond_refined_d	0.005
r_gen_planes_refined	0.004
r_bond_other_d	0.001
r_gen_planes_other	0.001

Non-Hydrogen Atoms Used in Refinement
Non-Hydrogen Atoms	Number
Protein Atoms	2386
Nucleic Acid Atoms
Solvent Atoms	54
Heterogen Atoms

Software

Software
Software Name	Purpose
REFMAC	refinement
XSCALE	data scaling
XDS	data reduction
PHASER	phasing